The `update_order_meta` function should return updated order object after saving it: https://github.com/wp-graphql/wp-graphql-woocommerce/blob/24dede2b8925091d16bc48d85269ca021e9b7237/includes/data/mutation/class-checkout-mutation.php#L753 and the calling function needs to update its order object with the return value, otherwise it will keep using the old order object.